1. Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy
Junkang Rong, John E. Bowers, Stefan R. Schulze, Vijay N. Waghmare,
Carl J. Rogers, Gary J. Pierce, Hua Zhang, James C. Estill, and
Andrew H. Paterson
Huge Gap
Pi-Cheng Hsiu
Department of Computer Science and Information Engineering, National Taiwan University

2. Outline What research the paper did Why do this research
Which problems the research suffers from
How to do this research

3. Liger (獅虎) = Lion + Tiger

4. 再繁殖下去呢 Lineage 雄虎 + 雌獅 = 虎獅 雄獅 + 雌獅虎 = 獅獅虎 雄虎 + 雌獅虎 = 虎獅虎
雄獅 + 雌虎 = 獅虎
雄虎 + 雌獅 = 虎獅
再繁殖下去呢
雄獅 + 雌獅虎 =
獅獅虎
雄虎 + 雌獅虎 = 虎獅虎
雄獅 + 雌虎獅 = 獅虎獅
雄虎 + 雌虎獅 = 虎虎獅
(獅|虎)*(獅虎|虎獅)

5. Arabidopsis & Gossypium

6. Framework of This Paper
Common Ancestor
Arabidopsis
Gossypiums

7. Arabidopsis Small genome size 125 Mb
Complete genetic and physical maps
5 chromosomes (2001)
Short life cycle
about 6 weeks
Few repetitive DNA sequences
Mb = megabases (百萬對nucleotide base pairs )

8. Gossypium An appropriate system for studying paleopolyploids
Monoploid (13 chromosomes)
Diploid (e.g., G. trilobum and G. raimondii)
Tetraploid (e.g., G. hirsutum)
Octaploid [Wendel et. al., 2003]

9. Paleopolyploidization
Whole genome duplication events occurred in the history of evolution
An important evolutionary mechanism (S. Ohno, 1970)
Some evidence
Yeast: 108 years ago
Vertebrates: 2×108 years ago
Plants : particularly prevalent

10. Polyploidy ＋ = Autopolyploidy Allopolyploidy
Polyploids created by chromosome duplication within a species
Allopolyploidy
Polyploids created by hybridization between different species
I’m 小黑麥
I’m 黑麥
I’m 小麥 ＋ =

11. Genome Duplication A: a genome that has 22 genes
B: a genome duplication

12. Gene Loss
C: a genome duplication followed by significant gene losses

13. Diploidization

14. Gene Divergence
The duplication of a region of chromosome containing a (generally functional) gene

15. Conserved Synteny
A chromosome pair, one from each of two species that share at least one ortholog

16. Keys to Infer Inference of conserved synteny in pre-duplicated genome
What was the original order of blocks?
Nature of post-duplication rearrangements events
How many rearrangements have occurred since the duplication occurred?
Statistics of gene loss versus gene divergence

17. Reference Arabidopsis Genome Analysis
wikipedia
Wolfe, KH and D. Shields, Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: , 1997.
P. Dehal and J. L. Boore, Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate, PLoS Biol, Vol. 3, No. 10, 2005.

18. Thank You